#!/usr/bin/env bash

sc="../../../data/source_data"
des="../../../data/testing_data/1.Golden_data"
## Gencode
GCD=${sc}/GENCODE
# human
./prepare_gencode.sh ${GCD}/gencode.v25.lncRNA_transcripts.fa ${GCD}/gencode.v25.del_gene.long_noncoding_RNAs.gtf ${des}/gencode_human_5000
# mouse
./prepare_gencode.sh ${GCD}/gencode.vM11.lncRNA_transcripts.fa ${GCD}/gencode.vM11.del_gene.long_noncoding_RNAs.gtf ${des}/gencode_mouse_5000

## refSeq
RF=${sc}/RefSeq
# human
./prepare_refSeq.sh ${RF}/Hs_mRNA_NM.fasta ${RF}/ref_GRCh38.p7_top_level.gff3 hs38 ${des}/refseq_human_5000
# mouse
./prepare_refSeq.sh ${RF}/Mm_mRNA_NM.fasta ${RF}/ref_GRCm38.p4_top_level.gff3 mm10 ${des}/refseq_mouse_5000